Re: [Freesurfer] peak MNI coordinates within a masked sig.mgh
External Email - Use Caution Thank you very much Prof Greve! I'm almost done! Now, using mri_volcluster I can identify the vertex number with highest significance within a ROI in a surface sig.mgh map (see attached txt). However I don't know how to compute the corresponding MNI coordinates of a specific vertex number (say 122288 in the file). I already checked the very helpful page https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems, but I did not see the precise calculation "from a single vertex number to (MNIx, MNIy,MNIz)". Maybe I missed something but the mri_volcluster output only displayed the vertex number (i.e no RAS coords) to work with. I am always working on fsaverage space. Thanks a lot in advance! On Tue, Sep 15, 2020 at 5:27 PM Douglas N. Greve wrote: > Use mri_annotation2label to convert the, eg, ?h.aparc.annot to a > segmentation (--seg output), then use mri_binarize with 1031. > > On 9/15/2020 10:41 AM, Fred Sampedro wrote: > > External Email - Use Caution > Thats precisely the point that I should be missing. To recap, I'm > interested in knowing the MNI coordinates of the vertex with highest > significance within a specific atlas-ROI (e.g. ctx-lh-supramarginal) from a > surface sig.mgh map (e.g. group comparison in cortical thickness). > > If I understood correctly, first I need a "surface binary mask" of the > atlas ROI, which I tried to get using mri_binarize but I am not sure if I > did it correctly. Then, I would fscalc mul the sig.mgh map with the surface > binary mask, and finally apply mri_volcluster. I'm stuck in the first step > of obtaining the desired surface binary mask from the default FS atlas. > > > > On Tue, Sep 15, 2020 at 4:10 PM Douglas N. Greve > wrote: > >> What do you mean you are trying to overlay it on lh.inflated? the output >> of mri_binarize will be a volume, so you'd have to sample it onto the >> surface in some way >> >> On 9/14/2020 9:28 AM, Fred Sampedro wrote: >> >> External Email - Use Caution >> Just a follow-up, I got stuck at trying to obtain a mask from binarizing >> a specific ROI from the aparc+aseg.mgz, aiming to mask my sig.mgh with this >> ROI.If for instance, I'd like to create a ROI from the left supramarginal >> gyrus, I found that its label is 1031. Now, I tried: >> >> mri_binarize --i aparc+aseg.mgz --o leftsupramarg.mgh --match 1031 >> >> however when visualizing the output of this command in freeview >> overlaying the mask on top of lh.inflated...it seems that this approach was >> wrong. >> >> Then looking at the mail archive I thought that this is somehow more >> complex, involving mri_annot2label, and mri_label2label with --outmask... >> however I tried for 2 days and did not obtain a convincing binary ROI mgh >> file that I could fscalc with the sig.mgh, I got lost with several command >> params (srclabel/trglabel..). >> >> Could you please help me with exact commands? I'm sure this should be >> easy but I lost this battle!! >> Thanks a lot in advance >> >> On Tue, Aug 4, 2020 at 5:14 PM Fred Sampedro >> wrote: >> >>> Thanks a lot! >>> >>> I read the mri_volcluster doc, can you confirm that the TalX TalY TalZ >>> coordinates are those of the vertex with maximum intensity within the >>> cluster? (it could be those of the cluster's center of gravity) >>> >>> Finally, I would be very grateful if you could help me with minor >>> parameter tuning of the commands: >>> >>> >>> >>> 1) mri_binarize lh aparc --min LABEL/NUMBER_OF_SUPRAMARG?(how do I get >>> it?) --o roimask.mgh >>> >>> 2) fslcalc sig.mgh mult roimask.mgh -o maskedsig.mgh >>> >>> 3) mri_volcluster --in maskedsig.mgh --thmin 0.001 --sum output.txt >>> >>> >>> >>> >>> >>> Thanks a lot in advance! >>> >>> On Mon, Aug 3, 2020 at 4:40 PM Douglas N. Greve >>> wrote: >>> >>>> Try mri_volcluster. Pass you masked sig as the input and set --thmin >>>> 0.0001 and specify a summary file with --sum. I think that should work >>>> >>>> On 7/31/2020 9:38 AM, Fred Sampedro wrote: >>>> >>>> External Email - Use Caution >>>> Dear FS experts, >>>> >>>> I have a rather simple question: >>>> >>>> I would like to obtain the MNI coordinates of the most significant >>>> vertex in a sig.mgh map but within a specific ROI (for instance the left >>>> supramarginal region). >>
Re: [Freesurfer] peak MNI coordinates within a masked sig.mgh
External Email - Use Caution Thats precisely the point that I should be missing. To recap, I'm interested in knowing the MNI coordinates of the vertex with highest significance within a specific atlas-ROI (e.g. ctx-lh-supramarginal) from a surface sig.mgh map (e.g. group comparison in cortical thickness). If I understood correctly, first I need a "surface binary mask" of the atlas ROI, which I tried to get using mri_binarize but I am not sure if I did it correctly. Then, I would fscalc mul the sig.mgh map with the surface binary mask, and finally apply mri_volcluster. I'm stuck in the first step of obtaining the desired surface binary mask from the default FS atlas. On Tue, Sep 15, 2020 at 4:10 PM Douglas N. Greve wrote: > What do you mean you are trying to overlay it on lh.inflated? the output > of mri_binarize will be a volume, so you'd have to sample it onto the > surface in some way > > On 9/14/2020 9:28 AM, Fred Sampedro wrote: > > External Email - Use Caution > Just a follow-up, I got stuck at trying to obtain a mask from binarizing a > specific ROI from the aparc+aseg.mgz, aiming to mask my sig.mgh with this > ROI.If for instance, I'd like to create a ROI from the left supramarginal > gyrus, I found that its label is 1031. Now, I tried: > > mri_binarize --i aparc+aseg.mgz --o leftsupramarg.mgh --match 1031 > > however when visualizing the output of this command in freeview overlaying > the mask on top of lh.inflated...it seems that this approach was wrong. > > Then looking at the mail archive I thought that this is somehow more > complex, involving mri_annot2label, and mri_label2label with --outmask... > however I tried for 2 days and did not obtain a convincing binary ROI mgh > file that I could fscalc with the sig.mgh, I got lost with several command > params (srclabel/trglabel..). > > Could you please help me with exact commands? I'm sure this should be easy > but I lost this battle!! > Thanks a lot in advance > > On Tue, Aug 4, 2020 at 5:14 PM Fred Sampedro > wrote: > >> Thanks a lot! >> >> I read the mri_volcluster doc, can you confirm that the TalX TalY TalZ >> coordinates are those of the vertex with maximum intensity within the >> cluster? (it could be those of the cluster's center of gravity) >> >> Finally, I would be very grateful if you could help me with minor >> parameter tuning of the commands: >> >> >> >> 1) mri_binarize lh aparc --min LABEL/NUMBER_OF_SUPRAMARG?(how do I get >> it?) --o roimask.mgh >> >> 2) fslcalc sig.mgh mult roimask.mgh -o maskedsig.mgh >> >> 3) mri_volcluster --in maskedsig.mgh --thmin 0.001 --sum output.txt >> >> >> >> >> >> Thanks a lot in advance! >> >> On Mon, Aug 3, 2020 at 4:40 PM Douglas N. Greve >> wrote: >> >>> Try mri_volcluster. Pass you masked sig as the input and set --thmin >>> 0.0001 and specify a summary file with --sum. I think that should work >>> >>> On 7/31/2020 9:38 AM, Fred Sampedro wrote: >>> >>> External Email - Use Caution >>> Dear FS experts, >>> >>> I have a rather simple question: >>> >>> I would like to obtain the MNI coordinates of the most significant >>> vertex in a sig.mgh map but within a specific ROI (for instance the left >>> supramarginal region). >>> >>> Here is my attempt but with practical gaps in terms of command >>> parameters: >>> >>> 1) mri_binarize lh aparc --min LABEL/NUMBER_OF_SUPRAMARG? --o roimask.mgh >>> >>> 2) fslmaths sig.mgh mult roimask.mgh -o maskedsig.mgh >>> >>> 3) which command could I use to obtain the MNI coordinates of the peak >>> value in maskedsig.mgh? >>> >>> Thanks a lot in advance! >>> >>> ___ >>> Freesurfer mailing >>> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >>> ___ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> > ___ > Freesurfer mailing > listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] peak MNI coordinates within a masked sig.mgh
External Email - Use Caution Just a follow-up, I got stuck at trying to obtain a mask from binarizing a specific ROI from the aparc+aseg.mgz, aiming to mask my sig.mgh with this ROI.If for instance, I'd like to create a ROI from the left supramarginal gyrus, I found that its label is 1031. Now, I tried: mri_binarize --i aparc+aseg.mgz --o leftsupramarg.mgh --match 1031 however when visualizing the output of this command in freeview overlaying the mask on top of lh.inflated...it seems that this approach was wrong. Then looking at the mail archive I thought that this is somehow more complex, involving mri_annot2label, and mri_label2label with --outmask... however I tried for 2 days and did not obtain a convincing binary ROI mgh file that I could fscalc with the sig.mgh, I got lost with several command params (srclabel/trglabel..). Could you please help me with exact commands? I'm sure this should be easy but I lost this battle!! Thanks a lot in advance On Tue, Aug 4, 2020 at 5:14 PM Fred Sampedro wrote: > Thanks a lot! > > I read the mri_volcluster doc, can you confirm that the TalX TalY TalZ > coordinates are those of the vertex with maximum intensity within the > cluster? (it could be those of the cluster's center of gravity) > > Finally, I would be very grateful if you could help me with minor > parameter tuning of the commands: > > > > 1) mri_binarize lh aparc --min LABEL/NUMBER_OF_SUPRAMARG?(how do I get > it?) --o roimask.mgh > > 2) fslcalc sig.mgh mult roimask.mgh -o maskedsig.mgh > > 3) mri_volcluster --in maskedsig.mgh --thmin 0.001 --sum output.txt > > > > > > Thanks a lot in advance! > > On Mon, Aug 3, 2020 at 4:40 PM Douglas N. Greve > wrote: > >> Try mri_volcluster. Pass you masked sig as the input and set --thmin >> 0.0001 and specify a summary file with --sum. I think that should work >> >> On 7/31/2020 9:38 AM, Fred Sampedro wrote: >> >> External Email - Use Caution >> Dear FS experts, >> >> I have a rather simple question: >> >> I would like to obtain the MNI coordinates of the most significant vertex >> in a sig.mgh map but within a specific ROI (for instance the left >> supramarginal region). >> >> Here is my attempt but with practical gaps in terms of command parameters: >> >> 1) mri_binarize lh aparc --min LABEL/NUMBER_OF_SUPRAMARG? --o roimask.mgh >> >> 2) fslmaths sig.mgh mult roimask.mgh -o maskedsig.mgh >> >> 3) which command could I use to obtain the MNI coordinates of the peak >> value in maskedsig.mgh? >> >> Thanks a lot in advance! >> >> ___ >> Freesurfer mailing >> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] peak MNI coordinates within a masked sig.mgh
External Email - Use Caution Thanks a lot! I read the mri_volcluster doc, can you confirm that the TalX TalY TalZ coordinates are those of the vertex with maximum intensity within the cluster? (it could be those of the cluster's center of gravity) Finally, I would be very grateful if you could help me with minor parameter tuning of the commands: 1) mri_binarize lh aparc --min LABEL/NUMBER_OF_SUPRAMARG?(how do I get it?) --o roimask.mgh 2) fslcalc sig.mgh mult roimask.mgh -o maskedsig.mgh 3) mri_volcluster --in maskedsig.mgh --thmin 0.001 --sum output.txt Thanks a lot in advance! On Mon, Aug 3, 2020 at 4:40 PM Douglas N. Greve wrote: > Try mri_volcluster. Pass you masked sig as the input and set --thmin > 0.0001 and specify a summary file with --sum. I think that should work > > On 7/31/2020 9:38 AM, Fred Sampedro wrote: > > External Email - Use Caution > Dear FS experts, > > I have a rather simple question: > > I would like to obtain the MNI coordinates of the most significant vertex > in a sig.mgh map but within a specific ROI (for instance the left > supramarginal region). > > Here is my attempt but with practical gaps in terms of command parameters: > > 1) mri_binarize lh aparc --min LABEL/NUMBER_OF_SUPRAMARG? --o roimask.mgh > > 2) fslmaths sig.mgh mult roimask.mgh -o maskedsig.mgh > > 3) which command could I use to obtain the MNI coordinates of the peak > value in maskedsig.mgh? > > Thanks a lot in advance! > > ___ > Freesurfer mailing > listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] peak MNI coordinates within a masked sig.mgh
External Email - Use Caution Dear FS experts, I have a rather simple question: I would like to obtain the MNI coordinates of the most significant vertex in a sig.mgh map but within a specific ROI (for instance the left supramarginal region). Here is my attempt but with practical gaps in terms of command parameters: 1) mri_binarize lh aparc --min LABEL/NUMBER_OF_SUPRAMARG? --o roimask.mgh 2) fslmaths sig.mgh mult roimask.mgh -o maskedsig.mgh 3) which command could I use to obtain the MNI coordinates of the peak value in maskedsig.mgh? Thanks a lot in advance! ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Anatomical cluster description table from mri_glmfit-sim?
External Email - Use Caution Dear FS experts, From an statistical map obtained by mri_glmfit-sim, say a cache.th13.abs.sig.masked.mgh map, I would like to list all the significant regions from all clusters in the following intuitive way, for instance: Supramarginal gyrus: X vertices, X mm^2, peak T-value=X Superior frontal gyrus: Y vertices, Y mm^2, peak T-value=Y ... That is, the % of significant vertices in the statistical map belonging to each region of the default FS atlas. I know that the cache.th13.abs.sig.cluster.summary file "summarizes" each cluster by a label, but clearly large clusters are made of several different anatomical regions that I would like to report. In other words, I wonder if there's an easy way to obtain a cluster description report similar to the one provided by the xjview toolbox for voxelbased maps in MNI space. I know I could probably achieve it by scripting, i.e. but looping through each ROI extracted from an atlas in fsaverage space and applying a mask with the glmfit map and then computing the overlap and such. But probably there's an easir way, or someone has already thought about it. I tried to search about this topic in the archive but failed to find a clear solution, probably I was not searching by the appropriate words. Thanks a lot in advance, ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Mean baseline Cth for each subject in a cluster obtained from a spc analysis
Dear Freesurfer Experts, I ran a longitudinal Cth analysis and found a cluster with significant spc differences between two groups. It was easy to obtain the mean spc values in that cluster for all the subjects. However, I would also like to have a spreedsheet with the baseline mean Cth values in that cluster for all my subjects to correlate with other clinical measures. My attempt was: mri_segstats --i SPC_ANALYSIS_FOLDER/y.mgh --seg SPC_ANALYSIS_FOLDER/SUBANALYSIS/mc-z.abs.th13.sig.cluster.mgh --excludeid 0 --sum CTH_inSPC_cluster.sum But obviously this is not the correct way to obtain for each subject the mean Cth value in that cluster. Any help would be much appreciated! Thanks a lot in advance, Fred ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] running longitudinal TRACULA on a subset of already processed baseline DTI scans?
Dear TRACULA users, I ran near 100 subjects through the standard (cross-sectional) TRACULA pipeline. Some of them (about 70) have also a longitudinal DTI scan 1-year after the already processed scans. I would like to run longitudinal TRACULA to obtain for those 70 subjects longitudinal changes in FA/MD in the major white matter tracts. My question is: should I specify in the longitudinal dmrirc file that the 80 baseline subjects have already been processed? Will tracula already know it and not re-compute? Could you please provide a fully-working sample dmrirc file for this scenario so I could see the format? I’ve found this pdf https://ftp.nmr.mgh.harvard.edu/pub/docs/TraculaNov2013/tracula.workshop.v.pdf only but didn’t manage to solve my questions. Thanks a lot in advance, Fred Sampedro, PhD Hospital de Sant Pau (Barcelona) ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] TRACULA trac-all prep error
Dear TRACULA users, I'm trying to preprocess a DTI subject in TRACULA which has an already reconed-all error-free T1. I followed the tutorial, but trac-all -prep exited with errors very fast. Please find attached the log and error files, and the dmrirc. Also bvals and bvecs (were obtained from dcm2nii). The raw dti.nii.gz has 16 volumes, the first being b0 and then 15 directions. Any ideas on what could be happening would be much appreciated, Thanks a lot in advance, Fred- dmrirc.tutorial Description: Binary data dtipd1467690.bval Description: Binary data dtipd1467690.bvec Description: Binary data trac-all.error Description: Binary data jue sep 21 11:49:35 CEST 2017 /media/freds/LinuxData/TRACULA_HSP/diffusion_tutorial /usr/local/freesurfer/bin/trac-all -prep -c dmrirc.tutorial Subject t1pd1467690 SUBJECTS_DIR /media/freds/LinuxData/TRACULA_HSP/diffusion_recons FREESURFER_HOME /usr/local/freesurfer Actual FREESURFER_HOME /usr/local/freesurfer build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c freds utm Linux utm 4.4.0-96-generic #119-Ubuntu SMP Tue Sep 12 14:59:54 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize8192 kbytes coredumpsize 0 kbytes memoryuseunlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 127247 maxlocks unlimited maxsignal127247 maxmessage 819200 maxnice 0 maxrtprio0 maxrttimeunlimited totalusedfree shared buff/cache available Mem: 32622380 881758812764464 140681104032823313740 Swap: 3998716 0 3998716 Program versions: $Id: trac-all,v 1.60.2.1 2016/12/20 17:04:05 zkaufman Exp $ mri_convert.bin --all-info ProgramName: mri_convert.bin ProgramArguments: --all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/21-09:49:35-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ User: freds Machine: utm Platform: Linux PlatformVersion: 4.4.0-96-generic CompilerName: GCC CompilerVersion: 40400 FLIRT version 6.0 $Id: bbregister,v 1.75 2016/05/10 20:02:28 greve Exp $ $Id: mri_cvs_register,v 1.48 2016/03/06 21:31:56 lzollei Exp $ ProgramName: dmri_motion ProgramArguments: --all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/21-09:49:35-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: User: freds Machine: utm Platform: Linux PlatformVersion: 4.4.0-96-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: dmri_train ProgramArguments: --all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/21-09:49:35-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: User: freds Machine: utm Platform: Linux PlatformVersion: 4.4.0-96-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: dmri_paths ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2017/09/21-09:49:35-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: User: freds Machine: utm Platform: Linux PlatformVersion: 4.4.0-96-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: dmri_pathstats ProgramArguments: --all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/21-09:49:35-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: User: freds Machine: utm Platform: Linux PlatformVersion: 4.4.0-96-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: dmri_mergepaths ProgramArguments: --all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/09/21-09:49:35-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: User: freds Machine: utm Platform: Linux PlatformVersion: 4.4.0-96-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: dmri_group ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2017/09/21-09:49:35-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: User: freds Machine: utm Platform: Linux PlatformVersion: 4.4.0-96-generic CompilerName: GCC CompilerVersion: 40400 New invocation of trac-preproc freds utm Linux utm 4.4.0-96-generic #119-Ubuntu SMP Tue Sep 12 14:59:54 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize8192 kbytes coredumpsize 0 kbytes memoryuseunlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 127247 maxlocks unlimited maxsignal127247 maxmessage 819200 maxnice 0 maxrtprio0 maxrttimeunlimited totalusedfree shared buff/cache available Mem: 32622380 882148812760508 140681104038423309868 Swap: 3998716 0 3998716 #- /usr/local/freesurfer/bin/trac-preproc #- #@# Image corrections jue sep 21 11:49:35 CEST 2017 mri_convert --bvec-voxel
Re: [Freesurfer] bbregister problem in FS5.1
Hi Douglas, Thanks a lot for your help, I understand. I tried replacing the mri_convert in 5.1 from the 5.3 and the bbregister command went a little bit further. Unfortunately, it segfaulted again when computing the relative costs. I'm attaching the output of the same command in 5.3 and in 5.1. Until the "Loading mov" in line 210, the output is actually the same. Could it be related to errors regarding the reading of the PET image? If anyone could help me figuring out which instruction is failing so I could try to replace it with the 5.3 version I would be very grateful. Thanks a lot in advance, Fred On Tue, Jul 26, 2016 at 1:30 AM, Douglas Greve <gr...@nmr.mgh.harvard.edu> wrote: > Sorry, I have no idea and I'm not going to try to dig in to 5.1 to see. > You can just copy mri_convert from 5.3 into 5.1 (make a backup first) > > On 7/25/16 12:31 PM, Fred Sampedro wrote: > > Hi Douglas, > > Thank you very much for answering. Unfortunately, I can read all the files > without any problem in FSL/SPM, and I still have more than 40GB of free > space. In fact, running the exact same instruction in freesurfer 5.3 works > fine. > > :( > > > > On Mon, Jul 25, 2016 at 5:21 PM, Douglas Greve <gr...@nmr.mgh.harvard.edu> > wrote: > >> It looks like one of two things: >> >> 1. The files SUBJ_ID.nii.gz is corrupted. See if another tool (FSL, SPM, >> AFNI) can read the file >> >> 2. You have run out of disk space >> >> On 7/24/16 10:52 AM, Fred Sampedro wrote: >> >> Dear FS experts, >> >> I've installed freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 and I'm >> trying to run bbregister to register a AV45-PET image to its corresponding >> FS processed T1 image. For that, I'm trying to run: >> >> bbregister --s SUBJ_ID --mov SUBJ_PET --reg register.dat --init-fsl --t1 >> >> And I keep getting segfaults: >> >> Log file is register.dat.log >> dom jul 24 16:44:19 CEST 2016 >> >> $Id: bbregister,v 1.49 2011/03/06 23:38:41 greve Exp $ >> Linux fredlab 3.16.0-30-generic #40~14.04.1-Ubuntu SMP Thu Jan 15 >> 17:43:14 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux >> FREESURFER_HOME /usr/local/freesurfer >> mri_convert ./allpets/SUBJ_ID/SUBJ_ID.nii.gz >> ./tmp.bbregister.5353/template.nii >> mri_convert ./allpets/SUBJ_ID/SUBJ_ID.nii.gz >> ./tmp.bbregister.5353/template.nii >> Segmentation fault (core dumped) >> >> >> I have tried the same installation and command in two different computers >> and obtained the same segfault. I have also tried the same pipeline using >> instead the FS version freesurfer-Linux-centos4-stable-pub-v5.1.0.tar.gz >> and get the same result. I didn't have this issue using freesurfer 5.3, but >> I need to use 5.1 for an ongoing project. >> >> I'm in an Ubuntu 14.04 LTS with 3.6GB of Memory, Processor Intel Core 2 >> Duo 3.0GHz, Graphics Intel Q45/Q43 OS type 64 bits. >> >> Any help would be much appreciated, >> >> Thanks a lot in advance, >> >> Fred Sampedro >> >> >> ___ >> Freesurfer mailing >> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> The information in this e-mail is intended only for the person to whom it >> is >> addressed. If you believe this e-mail was sent to you in error and the >> e-mail >> contains patient information, please contact the Partners Compliance >> HelpLine at >> http://www.partners.org/complianceline . If the e-mail was sent to you >> in error >> but does not contain patient information, please contact the sender and >> properly >> dispose of the e-mail. >> >> > > > ___ > Freesurfer mailing > listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was se
Re: [Freesurfer] bbregister problem in FS5.1
Hi Douglas, Thank you very much for answering. Unfortunately, I can read all the files without any problem in FSL/SPM, and I still have more than 40GB of free space. In fact, running the exact same instruction in freesurfer 5.3 works fine. :( On Mon, Jul 25, 2016 at 5:21 PM, Douglas Greve <gr...@nmr.mgh.harvard.edu> wrote: > It looks like one of two things: > > 1. The files SUBJ_ID.nii.gz is corrupted. See if another tool (FSL, SPM, > AFNI) can read the file > > 2. You have run out of disk space > > On 7/24/16 10:52 AM, Fred Sampedro wrote: > > Dear FS experts, > > I've installed freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 and I'm > trying to run bbregister to register a AV45-PET image to its corresponding > FS processed T1 image. For that, I'm trying to run: > > bbregister --s SUBJ_ID --mov SUBJ_PET --reg register.dat --init-fsl --t1 > > And I keep getting segfaults: > > Log file is register.dat.log > dom jul 24 16:44:19 CEST 2016 > > $Id: bbregister,v 1.49 2011/03/06 23:38:41 greve Exp $ > Linux fredlab 3.16.0-30-generic #40~14.04.1-Ubuntu SMP Thu Jan 15 17:43:14 > UTC 2015 x86_64 x86_64 x86_64 GNU/Linux > FREESURFER_HOME /usr/local/freesurfer > mri_convert ./allpets/SUBJ_ID/SUBJ_ID.nii.gz > ./tmp.bbregister.5353/template.nii > mri_convert ./allpets/SUBJ_ID/SUBJ_ID.nii.gz > ./tmp.bbregister.5353/template.nii > Segmentation fault (core dumped) > > > I have tried the same installation and command in two different computers > and obtained the same segfault. I have also tried the same pipeline using > instead the FS version freesurfer-Linux-centos4-stable-pub-v5.1.0.tar.gz > and get the same result. I didn't have this issue using freesurfer 5.3, but > I need to use 5.1 for an ongoing project. > > I'm in an Ubuntu 14.04 LTS with 3.6GB of Memory, Processor Intel Core 2 > Duo 3.0GHz, Graphics Intel Q45/Q43 OS type 64 bits. > > Any help would be much appreciated, > > Thanks a lot in advance, > > Fred Sampedro > > > ___ > Freesurfer mailing > listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] bbregister problem in FS5.1
Dear FS experts, I've installed freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 and I'm trying to run bbregister to register a AV45-PET image to its corresponding FS processed T1 image. For that, I'm trying to run: bbregister --s SUBJ_ID --mov SUBJ_PET --reg register.dat --init-fsl --t1 And I keep getting segfaults: Log file is register.dat.log dom jul 24 16:44:19 CEST 2016 $Id: bbregister,v 1.49 2011/03/06 23:38:41 greve Exp $ Linux fredlab 3.16.0-30-generic #40~14.04.1-Ubuntu SMP Thu Jan 15 17:43:14 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /usr/local/freesurfer mri_convert ./allpets/SUBJ_ID/SUBJ_ID.nii.gz ./tmp.bbregister.5353/template.nii mri_convert ./allpets/SUBJ_ID/SUBJ_ID.nii.gz ./tmp.bbregister.5353/template.nii Segmentation fault (core dumped) I have tried the same installation and command in two different computers and obtained the same segfault. I have also tried the same pipeline using instead the FS version freesurfer-Linux-centos4-stable-pub-v5.1.0.tar.gz and get the same result. I didn't have this issue using freesurfer 5.3, but I need to use 5.1 for an ongoing project. I'm in an Ubuntu 14.04 LTS with 3.6GB of Memory, Processor Intel Core 2 Duo 3.0GHz, Graphics Intel Q45/Q43 OS type 64 bits. Any help would be much appreciated, Thanks a lot in advance, Fred Sampedro ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] From NIfTI T1 to its volume cortical thickness map in MNI152 space.
Hi again, Any suggestions at least conceptual to the path I should follow to obtain cortical thickness volumetric data in MNI space? Thanks! On Sun, Jun 8, 2014 at 6:54 PM, Fred Sampedro fredsampe...@gmail.com wrote: Dear FreeSurfer experts, I am interested in analyzing group differences in cortical thickness with an application-specific GLM model that is build to work on MNI152 volume data. For that, my plan is to obtain a cortical thickness volume in MNI152 space for each of my MRI scans. My input data are nifti T1 scans. Here is my pipeline proposal for each T1 scan: INPUT: FOO_SUBJECT.nii FREESURFER CALLS (in $SUBJECTS_DIR): 1) recon-all -i FOO_SUBJECT.nii -subjid foosub 2) recon-all -all -subjid foosub 3) mri_surf2vol --surfvalpath /foosub/surf/lh.thickness --o foosub_cth_vol_lh #(?) 4) mri_surf2vol --surfvalpath /foosub/surf/rh.thickness --o foosub_cth_vol_rh #(?) 5) #should I merge lh and rh (?) how (?) let it be foosub_cth_vol 6) fslregister --s foosub_cth_vol --mov /path/to/TT_avg152T1.nii --reg TT_avg152T1_to_fsaverage.dat #should I convert it to MNI152 space (?) and how (?) 6) mri_fwhm --i foosub_cth_vol --o smoothed_foosub_cth_vol # should I smooth it (?) and how (?) OUTPUT to statistical analysis: smoothed_foosub_cth_vol (?) As you can see, I am pretty new to freesurfer and I have a lot of technical and conceptual gaps in this pipeline. Any advice on how to robustly accomplish this task would be much appreciated, as well as any advice regarding whether it would be a bad idea to try to carry out this kind of procedure in the first place. The context of the application is to apply the same ad-hoc statistical groupal analysis to PET, VBM GM, and cortical thickness data for all subjects. Thanks a lot in advance, Fred Sampedro ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] From NIfTI T1 to its volume cortical thickness map in MNI152 space.
Dear FreeSurfer experts, I am interested in analyzing group differences in cortical thickness with an application-specific GLM model that is build to work on MNI152 volume data. For that, my plan is to obtain a cortical thickness volume in MNI152 space for each of my MRI scans. My input data are nifti T1 scans. Here is my pipeline proposal for each T1 scan: INPUT: FOO_SUBJECT.nii FREESURFER CALLS (in $SUBJECTS_DIR): 1) recon-all -i FOO_SUBJECT.nii -subjid foosub 2) recon-all -all -subjid foosub 3) mri_surf2vol --surfvalpath /foosub/surf/lh.thickness --o foosub_cth_vol_lh #(?) 4) mri_surf2vol --surfvalpath /foosub/surf/rh.thickness --o foosub_cth_vol_rh #(?) 5) #should I merge lh and rh (?) how (?) let it be foosub_cth_vol 6) fslregister --s foosub_cth_vol --mov /path/to/TT_avg152T1.nii --reg TT_avg152T1_to_fsaverage.dat #should I convert it to MNI152 space (?) and how (?) 6) mri_fwhm --i foosub_cth_vol --o smoothed_foosub_cth_vol # should I smooth it (?) and how (?) OUTPUT to statistical analysis: smoothed_foosub_cth_vol (?) As you can see, I am pretty new to freesurfer and I have a lot of technical and conceptual gaps in this pipeline. Any advice on how to robustly accomplish this task would be much appreciated, as well as any advice regarding whether it would be a bad idea to try to carry out this kind of procedure in the first place. The context of the application is to apply the same ad-hoc statistical groupal analysis to PET, VBM GM, and cortical thickness data for all subjects. Thanks a lot in advance, Fred Sampedro ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Desikan atlas in MNI space (in a nii file)?
Dear FreeSurfer users, I am searching for the Desikan atlas (which I have in the tailarach space) in the MNI space, as a file (Desikan_mni.nii). I am aware that transforming from one space to the other is not a very good idea but nevertheless I would like to test some computations. Anyone can attach/send a link/know of if exists such a file? Thanks a lot Fred Sampedro Hospital de Sant Pau (Barcelona) ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
